MAVEQC is a flexible R-package that provides QC analysis of Saturation Genome Editing (SGE) experimental data. Available under GPL 3.0 from https://github.com/wtsi-hgi/MAVEQC
Displays QC plots and statistics for all samples for QC.
Displays the percentage of reads for each sample, based on 50 nucleotide increments.
Missing variants in the library
Displays the total number of reads per sample. Filtering based on 1-dimensional Kmean clustering that excludes unique sequences with low read counts.
Displays the percentage of library reads vs non-library reads (ie. Reference, PAM and Unmapped) for Accepted Reads.
Defines the mean read count per template oligo sequence.
Distribution of variants across targeton region based on log2(count+1) values.
Displays distribution of “LOF” (loss-of-function) vs all “Other” variants across the targeton region, based on read percentages for reference timepoint. Requires concordant distribution of LOF and Other variants.
condition_D7_vs_D4
condition_D15_vs_D4
Summarising the final results, below are the cutoffs using for PASS/FAIL